No he's using the Force to mask his true appearance. His old master, Darth Plagueis, discovered a method to control midichlorians and create life. At least, this is all according to ROTS spoilers. I believe they are true.

Anyway there is a 20 year difference (or something like that) between III and VI, so the difference in appearance will either be explained off as aging over time or something else...the movie's not even out yet, I believe it will be explained at some point. Hopefully.